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- PDB-4emg: Crystal structure of SpLsm3 -

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Basic information

Entry
Database: PDB / ID: 4emg
TitleCrystal structure of SpLsm3
ComponentsProbable U6 snRNA-associated Sm-like protein LSm3
KeywordsRNA BINDING PROTEIN / Sm fold / mRNA decay / Lsm proteins
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / chromosome, telomeric repeat region / Lsm1-7-Pat1 complex / U6 snRNP / telomerase holoenzyme complex / telomerase RNA binding / P-body assembly / U2 snRNP / precatalytic spliceosome ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / chromosome, telomeric repeat region / Lsm1-7-Pat1 complex / U6 snRNP / telomerase holoenzyme complex / telomerase RNA binding / P-body assembly / U2 snRNP / precatalytic spliceosome / RNA folding / U5 snRNP / U2 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / P-body / mRNA splicing, via spliceosome / chromatin binding / nucleolus / RNA binding / nucleus
Similarity search - Function
Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Probable U6 snRNA-associated Sm-like protein LSm3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsJiang, S.M. / Wu, D.H. / Song, H.W.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe.
Authors: Wu, D.H. / Jiang, S.M. / Bowler, M.W. / Song, H.W.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable U6 snRNA-associated Sm-like protein LSm3
B: Probable U6 snRNA-associated Sm-like protein LSm3
C: Probable U6 snRNA-associated Sm-like protein LSm3
D: Probable U6 snRNA-associated Sm-like protein LSm3
E: Probable U6 snRNA-associated Sm-like protein LSm3
F: Probable U6 snRNA-associated Sm-like protein LSm3
G: Probable U6 snRNA-associated Sm-like protein LSm3
H: Probable U6 snRNA-associated Sm-like protein LSm3
I: Probable U6 snRNA-associated Sm-like protein LSm3
J: Probable U6 snRNA-associated Sm-like protein LSm3
K: Probable U6 snRNA-associated Sm-like protein LSm3
L: Probable U6 snRNA-associated Sm-like protein LSm3
M: Probable U6 snRNA-associated Sm-like protein LSm3
N: Probable U6 snRNA-associated Sm-like protein LSm3


Theoretical massNumber of molelcules
Total (without water)151,49214
Polymers151,49214
Non-polymers00
Water2,594144
1
A: Probable U6 snRNA-associated Sm-like protein LSm3
B: Probable U6 snRNA-associated Sm-like protein LSm3
C: Probable U6 snRNA-associated Sm-like protein LSm3
D: Probable U6 snRNA-associated Sm-like protein LSm3
E: Probable U6 snRNA-associated Sm-like protein LSm3
F: Probable U6 snRNA-associated Sm-like protein LSm3
G: Probable U6 snRNA-associated Sm-like protein LSm3


Theoretical massNumber of molelcules
Total (without water)75,7467
Polymers75,7467
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Probable U6 snRNA-associated Sm-like protein LSm3
I: Probable U6 snRNA-associated Sm-like protein LSm3
J: Probable U6 snRNA-associated Sm-like protein LSm3
K: Probable U6 snRNA-associated Sm-like protein LSm3
L: Probable U6 snRNA-associated Sm-like protein LSm3
M: Probable U6 snRNA-associated Sm-like protein LSm3
N: Probable U6 snRNA-associated Sm-like protein LSm3


Theoretical massNumber of molelcules
Total (without water)75,7467
Polymers75,7467
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.430, 101.700, 143.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 9:55 OR RESSEQ 70:92 )
211CHAIN B AND (RESSEQ 9:55 OR RESSEQ 70:92 )
311CHAIN C AND (RESSEQ 9:55 OR RESSEQ 70:92 )
411CHAIN D AND (RESSEQ 9:55 OR RESSEQ 70:92 )
511CHAIN E AND (RESSEQ 9:55 OR RESSEQ 70:92 )
611CHAIN F AND (RESSEQ 9:55 OR RESSEQ 70:92 )
711CHAIN G AND (RESSEQ 9:55 OR RESSEQ 70:92 )
811CHAIN H AND (RESSEQ 9:55 OR RESSEQ 70:92 )
911CHAIN I AND (RESSEQ 9:55 OR RESSEQ 70:92 )
1011CHAIN J AND (RESSEQ 9:55 OR RESSEQ 70:92 )
1111CHAIN K AND (RESSEQ 9:55 OR RESSEQ 70:92 )
1211CHAIN L AND (RESSEQ 9:55 OR RESSEQ 70:92 )
1311CHAIN M AND (RESSEQ 9:55 OR RESSEQ 70:92 )
1411CHAIN N AND (RESSEQ 9:55 OR RESSEQ 70:92 )

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Components

#1: Protein
Probable U6 snRNA-associated Sm-like protein LSm3


Mass: 10820.833 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: lsm3, SPBC9B6.05c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y7M4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, pH 6.5, 0.2M MgCl2, 40% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→64.216 Å / Num. obs: 41387 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.75 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→64.216 Å / SU ML: 0.41 / σ(F): 7.91 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2010 4.86 %Random
Rwork0.2431 ---
all0.2447 ---
obs0.2447 41212 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.879 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.2708 Å20 Å2-0 Å2
2--6.9097 Å20 Å2
3----2.6389 Å2
Refinement stepCycle: LAST / Resolution: 2.7→64.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 0 144 8236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018204
X-RAY DIFFRACTIONf_angle_d1.24811074
X-RAY DIFFRACTIONf_dihedral_angle_d16.8223164
X-RAY DIFFRACTIONf_chiral_restr0.0781288
X-RAY DIFFRACTIONf_plane_restr0.0041428
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A570X-RAY DIFFRACTIONPOSITIONAL
12B570X-RAY DIFFRACTIONPOSITIONAL0.051
13C570X-RAY DIFFRACTIONPOSITIONAL0.053
14D570X-RAY DIFFRACTIONPOSITIONAL0.05
15E570X-RAY DIFFRACTIONPOSITIONAL0.057
16F570X-RAY DIFFRACTIONPOSITIONAL0.057
17G570X-RAY DIFFRACTIONPOSITIONAL0.059
18H570X-RAY DIFFRACTIONPOSITIONAL0.057
19I570X-RAY DIFFRACTIONPOSITIONAL0.048
110J570X-RAY DIFFRACTIONPOSITIONAL0.047
111K570X-RAY DIFFRACTIONPOSITIONAL0.051
112L570X-RAY DIFFRACTIONPOSITIONAL0.048
113M570X-RAY DIFFRACTIONPOSITIONAL0.056
114N570X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.79650.36851990.3353885100
2.7965-2.90850.31111980.30863892100
2.9085-3.04080.351950.28233867100
3.0408-3.20120.29742000.25653932100
3.2012-3.40170.27812000.23423900100
3.4017-3.66430.25351980.20943911100
3.6643-4.0330.22972030.20033913100
4.033-4.61650.21572060.18053973100
4.6165-5.81570.2472020.2113986100
5.8157-64.23410.31132090.3068411899

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